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env.yml
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env.yml
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name: degex
channels:
- conda-forge
- pytorch
- fastai
- dsm-72
- bioconda
dependencies:
- python==3.11
# PyTorch & Deep Learning
# --------------------------------------------------------------------------------
- pytorch
- pytorch-lightning
# Utilities
# --------------------------------------------------------------------------------
- tqdm
- pyyaml
# Packaging
# --------------------------------------------------------------------------------
# NOTE: for uploading to PyPI
- twine
# NOTE: for uploading to Anaconda Cloud
- anaconda-client
# NOTE: for building conda packages and conda-plugins
- conda
# NOTE: for building conda packages and conda-plugin
- conda-forge::conda-build
# Jupyter Notebooks
# --------------------------------------------------------------------------------
- conda-forge::notebook
- conda-forge::ipykernel
- conda-forge::ipywidgets
- conda-forge::jupyterlab
# nbdev
# --------------------------------------------------------------------------------
- fastai::nbdev>=2.3.12
# Data Science
# --------------------------------------------------------------------------------
- conda-forge::scikit-learn
- pandas
- numpy
- scipy
# Plotting
# --------------------------------------------------------------------------------
- conda-forge::matplotlib
- conda-forge::seaborn
- leidenalg
- graphtools
# single-cell related
- conda-forge::scanpy==1.9.2
- conda-forge::anndata==0.8.0
- bioconda::scprep=1.2.2
- bioconda::phate=1.0.10
- bioconda::gseapy
# do pip last to prevent as many conflicts as possible
- pip
- pip:
- magic-impute
- meld
- DiffusionEMD
- scrublet